New case study: genomic breeding for healthier, more resilient salmon

Optimising genomic selection in salmon breeding to improve the accuracy and affordability of the technology

Sea lice and gill disease are both challenges facing salmon farming. Rising water temperatures linked to climate change are expected to make these problems worse. Improving disease resistance through selective breeding is a high priority for sustainable aquaculture - but current genomic tools are often too expensive for widespread use.

Valued at £1.07m, the partners on this four-year project were Hendrix Genetics (formerly Landcatch Natural Selection), the Roslin Institute, the University of Stirling and Noahgene Ltd. The project was managed by SAIC.

The project set out to make genomic selection more accurate and affordable, enabling salmon breeders to produce fish with better gill health and resistance to sea lice. The team focused on two innovations:

1. Genotype imputation – a method that predicts missing genetic data, allowing breeders to use very low-cost genotyping without losing accuracy.
2. Functional genomic variants – adding key genetic markers linked to disease resistance to improve selection precision.

Using data from Hendrix Genetics, researchers tested these methods on salmon exposed to sea lice and gill disease. Results showed that similar accuracy to high-density genotyping could be achieved with as few as 200 genetic markers instead of tens of thousands - dramatically reducing costs. These findings pave the way for broader adoption of genomic selection, even in smaller aquaculture operations.

The project also explored the biology behind resistance. RNA sequencing revealed differences in immune responses between salmon resistant - and susceptible to - amoebic gill disease, identifying candidate genes for future breeding targets. In addition, a new gill scoring system was developed to better diagnose complex gill disorders and support breeding for multifactorial disease resistance.

The outcomes have influenced Hendrix Genetics’ breeding programmes in Scotland and Chile, enabling cost-effective genomic panels and more robust salmon strains. While genetic improvement is a gradual process, these advances promise long-term benefits: healthier fish, reduced treatment costs, and improved sustainability for global aquaculture.

The full title of this project is ‘Genomic breeding for gill health and lice resistance in salmon: improved accuracy and affordability’.

Read the full case study